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2017-04-06gnu: r-xml: Update to 3.98-1.6.Ricardo Wurmus
* gnu/packages/statistics.scm (r-xml): Update to 3.98-1.6.
2017-04-06gnu: r-rsqlite: Update to 1.1-2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rsqlite): Update to 1.1-2.
2017-04-06gnu: r-rmarkdown: Update to 1.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.4.
2017-04-06gnu: r-bbmisc: Update to 1.11.Ricardo Wurmus
* gnu/packages/statistics.scm (r-bbmisc): Update to 1.11.
2017-04-06gnu: r-backports: Update to 1.0.5.Ricardo Wurmus
* gnu/packages/statistics.scm (r-backports): Update to 1.0.5.
2017-04-06gnu: r-multitaper: Update to 1.0-13.Ricardo Wurmus
* gnu/packages/statistics.scm (r-multitaper): Update to 1.0-13.
2017-04-06gnu: r-xml2: Update to 1.1.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-xml2): Update to 1.1.1.
2017-04-06gnu: r-ade4: Update to 1.7-6.Ricardo Wurmus
* gnu/packages/statistics.scm (r-ade4): Update to 1.7-6.
2017-04-06gnu: r-data-table: Update to 1.10.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-data-table): Update to 1.10.4.
2017-04-06gnu: r-chron: Update to 2.3-50.Ricardo Wurmus
* gnu/packages/statistics.scm (r-chron): Update to 2.3-50.
2017-04-06gnu: r-cluster: Update to 2.0.6.Ricardo Wurmus
* gnu/packages/statistics.scm (r-cluster): Update to 2.0.6.
2017-04-06gnu: r-dbi: Update to 0.6-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dbi): Update to 0.6-1.
2017-04-06gnu: r-gdtools: Update to 0.1.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-gdtools): Update to 0.1.4.
2017-04-06gnu: r-stringr: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-stringr): Update to 1.2.0.
2017-04-06gnu: r-stringi: Update to 1.1.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-stringi): Update to 1.1.3.
2017-04-06gnu: r-rcpp: Update to 0.12.10.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpp): Update to 0.12.10.
2017-04-06gnu: r-digest: Update to 0.6.12.Ricardo Wurmus
* gnu/packages/statistics.scm (r-digest): Update to 0.6.12.
2017-04-06gnu: r-survival: Update to 2.41-3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-survival): Update to 2.41-3.
2017-04-06gnu: r-mgcv: Update to 1.8-17.Ricardo Wurmus
* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-17.
2017-04-06gnu: r-matrix: Update to 1.2-8.Ricardo Wurmus
* gnu/packages/statistics.scm (r-matrix): Update to 1.2-8.
2017-04-06gnu: r-lattice: Update to 0.20-35.Ricardo Wurmus
* gnu/packages/statistics.scm (r-lattice): Update to 0.20-35.
2017-04-06gnu: r-rprojroot: Update to 1.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rprojroot): Update to 1.2.
2017-04-06gnu: r-htmltable: Update to 1.9.Ricardo Wurmus
* gnu/packages/web.scm (r-htmltable): Update to 1.9. [propagated-inputs]: Add "r-checkmate" and "r-htmlwidgets".
2017-04-06gnu: r-curl: Update to 2.4.Ricardo Wurmus
* gnu/packages/web.scm (r-curl): Update to 2.4.
2017-04-06gnu: r-genomeinfodb: Update to 1.10.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.3. [propagated-inputs]: Add "r-rcurl".
2017-04-06gnu: r-xvector: Update to 0.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.1.
2017-04-06gnu: r-bioccheck: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.10.1. [propagated-inputs]: Remove "r-knitr" and "r-devtools".
2017-04-06gnu: r-tidyr: Update to 0.6.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tidyr): Update to 0.6.1. [propagated-inputs]: Add "r-tibble".
2017-04-06gnu: r-roxygen2: Update to 6.0.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-roxygen2): Update to 6.0.1. [propagated-inputs]: Add "r-commonmark", "r-desc", "r-r6", and "r-xml2".
2017-04-06gnu: Add r-commonmark.Ricardo Wurmus
* gnu/packages/statistics.scm (r-commonmark): New variable.
2017-04-06gnu: Add r-desc.Ricardo Wurmus
* gnu/packages/statistics.scm (r-desc): New variable.
2017-04-06gnu: r-readr: Update to 1.1.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-readr): Update to 1.1.0. [propagated-inputs]: Remove "r-curl".
2017-04-06gnu: r-tibble: Update to 1.3.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tibble): Update to 1.3.0. [propagated-inputs]: Remove "r-assertthat".
2017-04-06gnu: r-jsonlite: Update to 1.3.Ricardo Wurmus
* gnu/packages/web.scm (r-jsonlite): Update to 1.3.
2017-04-06gnu: ldc-bootstrap: Delete failing test.Ricardo Wurmus
* gnu/packages/ldc.scm (ldc-bootstrap)[arguments]: Delete failing test in build phase.
2017-04-06gnu: guile-aspell: Switch to Guile 2.2.Ludovic Courtès
* gnu/packages/guile.scm (guile-aspell)[inputs]: Replace GUILE-2.0 with GUILE-2.2.
2017-04-06gnu: guile-aspell: Remove hard-coded "site/2.0" from $(guilesitedir).Ludovic Courtès
* gnu/packages/guile.scm (guile-aspell)[arguments]: Remove #:configure-flags. Add 'set-guilesitedir' phase.
2017-04-06gnu: guile-aspell: Update to 0.4.Ludovic Courtès
* gnu/packages/guile.scm (guile-aspell): Update to 0.4. [arguments] <#:phases>: Adjust 'set-libaspell-file-name' to new source tree layout.
2017-04-06system: Support the --root option in 'guix system'.Chris Marusich
Fixes <https://bugs.gnu.org/26271>. * guix/scripts/system.scm (perform-action): Add #:gc-root parameter and honor it. (show-help): Document the --root option. (%options): Add 'root'. (process-action): Pass 'root' option to perform-action as #:gc-root. * doc/guix.texi (Invoking guix system): Document '--root'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-04-06build: Add and export procedure 'register-root*'.Chris Marusich
* guix/scripts/build.scm (register-root*): Add and export it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-04-05environment: Deal with single-entry search paths.Ludovic Courtès
This is a followup to fcd75bdbfa99d14363b905afbf914eec20e69df8. * guix/scripts/environment.scm (create-environment): Check whether SEPARATOR is #f.
2017-04-05doc: Add "Documentation" section.Ludovic Courtès
* doc/guix.texi (Documentation): New node.
2017-04-05profiles: Generate database file for man pages.Maxim Cournoyer
The mandb database file (index.db) is used by the "apropos" (whatis) or "man -k" commands. This change introduces a profile hook to generate such database file. * guix/profiles.scm (manual-database): New procedure. (%default-profile-hooks): Add it. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2017-04-05build-system/python: 'package-with-explicit-python' uses 'package-mapping'.Ludovic Courtès
* guix/build-system/python.scm (package-with-explicit-python) [package-variant, cut?]: New procedures. [transform]: Remove 'mlambdaq' form and input tuple handling. Use 'package-mapping'.
2017-04-05packages: Add 'package-mapping' and base 'package-input-rewriting' on it.Ludovic Courtès
* guix/packages.scm (package-mapping): New procedure. (package-input-rewriting): Rewrite in terms of 'package-mapping'. * tests/packages.scm ("package-mapping"): New test. * doc/guix.texi (Defining Packages): Document it.
2017-04-05Revert "gnu: openexr: Add IlmBase include sub-directory to 'OpenEXR.pc'."Ludovic Courtès
This reverts commit 01fe019166fe8a925b3bf3b489792b52b1b6ca7a, which was unneeded because IlmBase is already listed as 'Requires' in 'OpenEXR.pc'.
2017-04-05Revert "gnu: bc: Update to 1.07."Tobias Geerinckx-Rice
This reverts commit dfee7daedb760f1b1d7506829ca31633f4173356. It causes the linux-libre@4.9 build to hang (command-line usage works fine).
2017-04-05gnu: Move audacity to audio.scm.Kei Kebreau
* gnu/packages/audacity.scm: Remove file and move audacity... * gnu/packages/audio.scm: ...here. * gnu/local.mk: Remove reference to removed file.
2017-04-05import cran: Distinguish Bioconductor data packages.Ricardo Wurmus
* guix/import/cran.scm (bioconductor-package?): Exclude Bioconductor data packages. (bioconductor-data-package?): New procedure.
2017-04-05gnu: sra-tools: Fix glibc naming conflict.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Add build phase "patch-away-glibc-conflict" to fix a definition conflict with glibc 2.25.
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